Hi,
I would like to start using the MD and WormLikeChain functions in IMP, but I don't know what their current state is. Are they safe to use?
Thanks, Davide
MD gets used by various people and is in good shape . The WLC class hasn't been used in forever as far as I know, but worked fine last I looked at it.
On Wed, Oct 30, 2013 at 7:19 AM, Davide Baù davide.bau@gmail.com wrote:
> Hi, > > I would like to start using the MD and WormLikeChain functions in IMP, but > I don't know what their current state is. > Are they safe to use? > > Thanks, > Davide > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev >
Thanks Daniel!
> The WLC class hasn't been used in forever as far as I know, but worked fine last I looked at it.
Any possibility of having a example of how to use the WLC? I looked around but did not find any.
Thanks, Davide
> > > On Wed, Oct 30, 2013 at 7:19 AM, Davide Baù davide.bau@gmail.com wrote: > Hi, > > I would like to start using the MD and WormLikeChain functions in IMP, but I don't know what their current state is. > Are they safe to use? > > Thanks, > Davide > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
It is used like any other pair score. core:: create_restraint and container::create_restraint or core::PairRrestraint/container::PairsRestraint can be used to bind it to particle pairs to make a Restraint. The container::ConsecutivePairContainer is probably useful for generating a particle pairs list.
On Monday, November 4, 2013, Davide Baù wrote:
> Thanks Daniel! > > The WLC class hasn't been used in forever as far as I know, but worked > fine last I looked at it. > > > Any possibility of having a example of how to use the WLC? I looked around > but did not find any. > > Thanks, > Davide > > > > > > On Wed, Oct 30, 2013 at 7:19 AM, Davide Baù <davide.bau@gmail.com<javascript:_e({}, 'cvml', 'davide.bau@gmail.com');> > > wrote: > >> Hi, >> >> I would like to start using the MD and WormLikeChain functions in IMP, >> but I don't know what their current state is. >> Are they safe to use? >> >> Thanks, >> Davide >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org <javascript:_e({}, 'cvml', 'IMP-dev@salilab.org');> >> https://salilab.org/mailman/listinfo/imp-dev >> > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org <javascript:_e({}, 'cvml', 'IMP-dev@salilab.org');> > https://salilab.org/mailman/listinfo/imp-dev > > >
There's something I don't understand: if I use IMP.container.create_restraint(), I get the attribute error "AttributeError: 'module' object has no attribute 'create_restraint'", which I wasn't expecting.
Davide
On Nov 4, 2013, at 6:42 PM, Daniel Russel wrote:
> It is used like any other pair score. core:: create_restraint and container::create_restraint or core::PairRrestraint/container::PairsRestraint can be used to bind it to particle pairs to make a Restraint. The container::ConsecutivePairContainer is probably useful for generating a particle pairs list. > > On Monday, November 4, 2013, Davide Baù wrote: > Thanks Daniel! > >> The WLC class hasn't been used in forever as far as I know, but worked fine last I looked at it. > > Any possibility of having a example of how to use the WLC? I looked around but did not find any. > > Thanks, > Davide > > > >> >> >> On Wed, Oct 30, 2013 at 7:19 AM, Davide Baù davide.bau@gmail.com wrote: >> Hi, >> >> I would like to start using the MD and WormLikeChain functions in IMP, but I don't know what their current state is. >> Are they safe to use? >> >> Thanks, >> Davide >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
Sorry, the function is C++-only (as it is a template function). I could add a python version (at least should fix the docs).
On Wed, Nov 6, 2013 at 9:50 AM, Davide Baù davide.bau@gmail.com wrote:
> There's something I don't understand: if I > use IMP.container.create_restraint(), I get the attribute error > "AttributeError: 'module' object has no attribute 'create_restraint'", > which I wasn't expecting. > > Davide > > > > > On Nov 4, 2013, at 6:42 PM, Daniel Russel wrote: > > It is used like any other pair score. core:: create_restraint and > container::create_restraint or > core::PairRrestraint/container::PairsRestraint can be used to bind it to > particle pairs to make a Restraint. The container::ConsecutivePairContainer > is probably useful for generating a particle pairs list. > > On Monday, November 4, 2013, Davide Baù wrote: > >> Thanks Daniel! >> >> The WLC class hasn't been used in forever as far as I know, but worked >> fine last I looked at it. >> >> >> Any possibility of having a example of how to use the WLC? I looked >> around but did not find any. >> >> Thanks, >> Davide >> >> >> >> >> >> On Wed, Oct 30, 2013 at 7:19 AM, Davide Baù davide.bau@gmail.com wrote: >> >>> Hi, >>> >>> I would like to start using the MD and WormLikeChain functions in IMP, >>> but I don't know what their current state is. >>> Are they safe to use? >>> >>> Thanks, >>> Davide >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >>> >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >> >> >> _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > >
That would help, thanks!
On Nov 6, 2013, at 7:08 PM, Daniel Russel wrote:
> Sorry, the function is C++-only (as it is a template function). I could add a python version (at least should fix the docs). > > > On Wed, Nov 6, 2013 at 9:50 AM, Davide Baù davide.bau@gmail.com wrote: > There's something I don't understand: if I use IMP.container.create_restraint(), I get the attribute error "AttributeError: 'module' object has no attribute 'create_restraint'", which I wasn't expecting. > > Davide > > > > > On Nov 4, 2013, at 6:42 PM, Daniel Russel wrote: > >> It is used like any other pair score. core:: create_restraint and container::create_restraint or core::PairRrestraint/container::PairsRestraint can be used to bind it to particle pairs to make a Restraint. The container::ConsecutivePairContainer is probably useful for generating a particle pairs list. >> >> On Monday, November 4, 2013, Davide Baù wrote: >> Thanks Daniel! >> >>> The WLC class hasn't been used in forever as far as I know, but worked fine last I looked at it. >> >> Any possibility of having a example of how to use the WLC? I looked around but did not find any. >> >> Thanks, >> Davide >> >> >> >>> >>> >>> On Wed, Oct 30, 2013 at 7:19 AM, Davide Baù davide.bau@gmail.com wrote: >>> Hi, >>> >>> I would like to start using the MD and WormLikeChain functions in IMP, but I don't know what their current state is. >>> Are they safe to use? >>> >>> Thanks, >>> Davide >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
Just to add, for now just create a core::PairRestraint or containerPairsRestraint. The functionality is identical to what create_restraint would do in python (in C++ create_restraint can do cooler things with compile time binding).
On Thu, Nov 7, 2013 at 6:09 AM, Davide Baù davide.bau@gmail.com wrote:
> That would help, thanks! > > > On Nov 6, 2013, at 7:08 PM, Daniel Russel wrote: > > Sorry, the function is C++-only (as it is a template function). I could > add a python version (at least should fix the docs). > > > On Wed, Nov 6, 2013 at 9:50 AM, Davide Baù davide.bau@gmail.com wrote: > >> There's something I don't understand: if I >> use IMP.container.create_restraint(), I get the attribute error >> "AttributeError: 'module' object has no attribute 'create_restraint'", >> which I wasn't expecting. >> >> Davide >> >> >> >> >> On Nov 4, 2013, at 6:42 PM, Daniel Russel wrote: >> >> It is used like any other pair score. core:: create_restraint and >> container::create_restraint or >> core::PairRrestraint/container::PairsRestraint can be used to bind it to >> particle pairs to make a Restraint. The container::ConsecutivePairContainer >> is probably useful for generating a particle pairs list. >> >> On Monday, November 4, 2013, Davide Baù wrote: >> >>> Thanks Daniel! >>> >>> The WLC class hasn't been used in forever as far as I know, but worked >>> fine last I looked at it. >>> >>> >>> Any possibility of having a example of how to use the WLC? I looked >>> around but did not find any. >>> >>> Thanks, >>> Davide >>> >>> >>> >>> >>> >>> On Wed, Oct 30, 2013 at 7:19 AM, Davide Baù davide.bau@gmail.comwrote: >>> >>>> Hi, >>>> >>>> I would like to start using the MD and WormLikeChain functions in IMP, >>>> but I don't know what their current state is. >>>> Are they safe to use? >>>> >>>> Thanks, >>>> Davide >>>> _______________________________________________ >>>> IMP-dev mailing list >>>> IMP-dev@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-dev >>>> >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >>> >>> >>> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >> >> >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >> >> > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > >
Will do, thanks!
On Nov 7, 2013, at 5:21 PM, Daniel Russel wrote:
> Just to add, for now just create a core::PairRestraint or containerPairsRestraint. The functionality is identical to what create_restraint would do in python (in C++ create_restraint can do cooler things with compile time binding). > > > On Thu, Nov 7, 2013 at 6:09 AM, Davide Baù davide.bau@gmail.com wrote: > That would help, thanks! > > > On Nov 6, 2013, at 7:08 PM, Daniel Russel wrote: > >> Sorry, the function is C++-only (as it is a template function). I could add a python version (at least should fix the docs). >> >> >> On Wed, Nov 6, 2013 at 9:50 AM, Davide Baù davide.bau@gmail.com wrote: >> There's something I don't understand: if I use IMP.container.create_restraint(), I get the attribute error "AttributeError: 'module' object has no attribute 'create_restraint'", which I wasn't expecting. >> >> Davide >> >> >> >> >> On Nov 4, 2013, at 6:42 PM, Daniel Russel wrote: >> >>> It is used like any other pair score. core:: create_restraint and container::create_restraint or core::PairRrestraint/container::PairsRestraint can be used to bind it to particle pairs to make a Restraint. The container::ConsecutivePairContainer is probably useful for generating a particle pairs list. >>> >>> On Monday, November 4, 2013, Davide Baù wrote: >>> Thanks Daniel! >>> >>>> The WLC class hasn't been used in forever as far as I know, but worked fine last I looked at it. >>> >>> Any possibility of having a example of how to use the WLC? I looked around but did not find any. >>> >>> Thanks, >>> Davide >>> >>> >>> >>>> >>>> >>>> On Wed, Oct 30, 2013 at 7:19 AM, Davide Baù davide.bau@gmail.com wrote: >>>> Hi, >>>> >>>> I would like to start using the MD and WormLikeChain functions in IMP, but I don't know what their current state is. >>>> Are they safe to use? >>>> >>>> Thanks, >>>> Davide >>>> _______________________________________________ >>>> IMP-dev mailing list >>>> IMP-dev@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-dev >>>> >>>> _______________________________________________ >>>> IMP-dev mailing list >>>> IMP-dev@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-dev >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >> >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >> >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
Do I need to create a new PairScore class to use a WLC score with, e.g. container::PairsRestraint? I'm asking because the code works with existing PairScores, but they are mainly distance scores.
Davide
On Nov 7, 2013, at 5:21 PM, Daniel Russel wrote:
> Just to add, for now just create a core::PairRestraint or containerPairsRestraint. The functionality is identical to what create_restraint would do in python (in C++ create_restraint can do cooler things with compile time binding). > > > On Thu, Nov 7, 2013 at 6:09 AM, Davide Baù davide.bau@gmail.com wrote: > That would help, thanks! > > > On Nov 6, 2013, at 7:08 PM, Daniel Russel wrote: > >> Sorry, the function is C++-only (as it is a template function). I could add a python version (at least should fix the docs). >> >> >> On Wed, Nov 6, 2013 at 9:50 AM, Davide Baù davide.bau@gmail.com wrote: >> There's something I don't understand: if I use IMP.container.create_restraint(), I get the attribute error "AttributeError: 'module' object has no attribute 'create_restraint'", which I wasn't expecting. >> >> Davide >> >> >> >> >> On Nov 4, 2013, at 6:42 PM, Daniel Russel wrote: >> >>> It is used like any other pair score. core:: create_restraint and container::create_restraint or core::PairRrestraint/container::PairsRestraint can be used to bind it to particle pairs to make a Restraint. The container::ConsecutivePairContainer is probably useful for generating a particle pairs list. >>> >>> On Monday, November 4, 2013, Davide Baù wrote: >>> Thanks Daniel! >>> >>>> The WLC class hasn't been used in forever as far as I know, but worked fine last I looked at it. >>> >>> Any possibility of having a example of how to use the WLC? I looked around but did not find any. >>> >>> Thanks, >>> Davide >>> >>> >>> >>>> >>>> >>>> On Wed, Oct 30, 2013 at 7:19 AM, Davide Baù davide.bau@gmail.com wrote: >>>> Hi, >>>> >>>> I would like to start using the MD and WormLikeChain functions in IMP, but I don't know what their current state is. >>>> Are they safe to use? >>>> >>>> Thanks, >>>> Davide >>>> _______________________________________________ >>>> IMP-dev mailing list >>>> IMP-dev@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-dev >>>> >>>> _______________________________________________ >>>> IMP-dev mailing list >>>> IMP-dev@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-dev >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >> >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >> >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
Yes, you make a pair score from WLC (using either SphereDistancePairScore or DistancePairScore) and then create a restraint. The first part you would have to do with the create_restraint function anyway. Although it might be cool to add a create_distance_restraint function. But we don't have such a thing.
On Thu, Nov 7, 2013 at 8:51 AM, Davide Baù davide.bau@gmail.com wrote:
> Do I need to create a new PairScore class to use a WLC score with, e.g. > container::PairsRestraint? > I'm asking because the code works with existing PairScores, but they are > mainly distance scores. > > Davide > > > > > > On Nov 7, 2013, at 5:21 PM, Daniel Russel wrote: > > Just to add, for now just create a core::PairRestraint or > containerPairsRestraint. The functionality is identical to what > create_restraint would do in python (in C++ create_restraint can do cooler > things with compile time binding). > > > On Thu, Nov 7, 2013 at 6:09 AM, Davide Baù davide.bau@gmail.com wrote: > >> That would help, thanks! >> >> >> On Nov 6, 2013, at 7:08 PM, Daniel Russel wrote: >> >> Sorry, the function is C++-only (as it is a template function). I could >> add a python version (at least should fix the docs). >> >> >> On Wed, Nov 6, 2013 at 9:50 AM, Davide Baù davide.bau@gmail.com wrote: >> >>> There's something I don't understand: if I >>> use IMP.container.create_restraint(), I get the attribute error >>> "AttributeError: 'module' object has no attribute 'create_restraint'", >>> which I wasn't expecting. >>> >>> Davide >>> >>> >>> >>> >>> On Nov 4, 2013, at 6:42 PM, Daniel Russel wrote: >>> >>> It is used like any other pair score. core:: create_restraint and >>> container::create_restraint or >>> core::PairRrestraint/container::PairsRestraint can be used to bind it to >>> particle pairs to make a Restraint. The container::ConsecutivePairContainer >>> is probably useful for generating a particle pairs list. >>> >>> On Monday, November 4, 2013, Davide Baù wrote: >>> >>>> Thanks Daniel! >>>> >>>> The WLC class hasn't been used in forever as far as I know, but worked >>>> fine last I looked at it. >>>> >>>> >>>> Any possibility of having a example of how to use the WLC? I looked >>>> around but did not find any. >>>> >>>> Thanks, >>>> Davide >>>> >>>> >>>> >>>> >>>> >>>> On Wed, Oct 30, 2013 at 7:19 AM, Davide Baù davide.bau@gmail.comwrote: >>>> >>>>> Hi, >>>>> >>>>> I would like to start using the MD and WormLikeChain functions in IMP, >>>>> but I don't know what their current state is. >>>>> Are they safe to use? >>>>> >>>>> Thanks, >>>>> Davide >>>>> _______________________________________________ >>>>> IMP-dev mailing list >>>>> IMP-dev@salilab.org >>>>> https://salilab.org/mailman/listinfo/imp-dev >>>>> >>>> >>>> _______________________________________________ >>>> IMP-dev mailing list >>>> IMP-dev@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-dev >>>> >>>> >>>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >>> >>> >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >>> >>> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >> >> >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >> >> > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > >
Thanks Daniel!
Could you please provide a MD example too?
Davide
On Nov 7, 2013, at 6:31 PM, Daniel Russel wrote: > Yes, you make a pair score from WLC (using either SphereDistancePairScore or DistancePairScore) and then create a restraint. The first part you would have to do with the create_restraint function anyway. Although it might be cool to add a create_distance_restraint function. But we don't have such a thing. > > > On Thu, Nov 7, 2013 at 8:51 AM, Davide Baù davide.bau@gmail.com wrote: > Do I need to create a new PairScore class to use a WLC score with, e.g. container::PairsRestraint? > I'm asking because the code works with existing PairScores, but they are mainly distance scores. > > Davide > > > > > > On Nov 7, 2013, at 5:21 PM, Daniel Russel wrote: > >> Just to add, for now just create a core::PairRestraint or containerPairsRestraint. The functionality is identical to what create_restraint would do in python (in C++ create_restraint can do cooler things with compile time binding). >> >> >> On Thu, Nov 7, 2013 at 6:09 AM, Davide Baù davide.bau@gmail.com wrote: >> That would help, thanks! >> >> >> On Nov 6, 2013, at 7:08 PM, Daniel Russel wrote: >> >>> Sorry, the function is C++-only (as it is a template function). I could add a python version (at least should fix the docs). >>> >>> >>> On Wed, Nov 6, 2013 at 9:50 AM, Davide Baù davide.bau@gmail.com wrote: >>> There's something I don't understand: if I use IMP.container.create_restraint(), I get the attribute error "AttributeError: 'module' object has no attribute 'create_restraint'", which I wasn't expecting. >>> >>> Davide >>> >>> >>> >>> >>> On Nov 4, 2013, at 6:42 PM, Daniel Russel wrote: >>> >>>> It is used like any other pair score. core:: create_restraint and container::create_restraint or core::PairRrestraint/container::PairsRestraint can be used to bind it to particle pairs to make a Restraint. The container::ConsecutivePairContainer is probably useful for generating a particle pairs list. >>>> >>>> On Monday, November 4, 2013, Davide Baù wrote: >>>> Thanks Daniel! >>>> >>>>> The WLC class hasn't been used in forever as far as I know, but worked fine last I looked at it. >>>> >>>> Any possibility of having a example of how to use the WLC? I looked around but did not find any. >>>> >>>> Thanks, >>>> Davide >>>> >>>> >>>> >>>>> >>>>> >>>>> On Wed, Oct 30, 2013 at 7:19 AM, Davide Baù davide.bau@gmail.com wrote: >>>>> Hi, >>>>> >>>>> I would like to start using the MD and WormLikeChain functions in IMP, but I don't know what their current state is. >>>>> Are they safe to use? >>>>> >>>>> Thanks, >>>>> Davide >>>>> _______________________________________________ >>>>> IMP-dev mailing list >>>>> IMP-dev@salilab.org >>>>> https://salilab.org/mailman/listinfo/imp-dev >>>>> >>>>> _______________________________________________ >>>>> IMP-dev mailing list >>>>> IMP-dev@salilab.org >>>>> https://salilab.org/mailman/listinfo/imp-dev >>>> >>>> _______________________________________________ >>>> IMP-dev mailing list >>>> IMP-dev@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-dev >>> >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >>> >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >> >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >> >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
What aspect of MD would you like an example of? The MD class basically has two functions: one to set the time step and one to optimize. For the force field side there are already the charmm_forcefield examples. The bencmark_md_charmm.cpp provides a pretty simple example of using them together.
On Mon, Nov 11, 2013 at 3:44 AM, Davide Baù davide.bau@gmail.com wrote:
> Thanks Daniel! > > Could you please provide a MD example too? > > Davide > > > On Nov 7, 2013, at 6:31 PM, Daniel Russel wrote: > > Yes, you make a pair score from WLC (using either SphereDistancePairScore > or DistancePairScore) and then create a restraint. The first part you would > have to do with the create_restraint function anyway. Although it might be > cool to add a create_distance_restraint function. But we don't have such a > thing. > > > On Thu, Nov 7, 2013 at 8:51 AM, Davide Baù davide.bau@gmail.com wrote: > >> Do I need to create a new PairScore class to use a WLC score with, e.g. >> container::PairsRestraint? >> I'm asking because the code works with existing PairScores, but they are >> mainly distance scores. >> >> Davide >> >> >> >> >> >> On Nov 7, 2013, at 5:21 PM, Daniel Russel wrote: >> >> Just to add, for now just create a core::PairRestraint or >> containerPairsRestraint. The functionality is identical to what >> create_restraint would do in python (in C++ create_restraint can do cooler >> things with compile time binding). >> >> >> On Thu, Nov 7, 2013 at 6:09 AM, Davide Baù davide.bau@gmail.com wrote: >> >>> That would help, thanks! >>> >>> >>> On Nov 6, 2013, at 7:08 PM, Daniel Russel wrote: >>> >>> Sorry, the function is C++-only (as it is a template function). I could >>> add a python version (at least should fix the docs). >>> >>> >>> On Wed, Nov 6, 2013 at 9:50 AM, Davide Baù davide.bau@gmail.com wrote: >>> >>>> There's something I don't understand: if I >>>> use IMP.container.create_restraint(), I get the attribute error >>>> "AttributeError: 'module' object has no attribute 'create_restraint'", >>>> which I wasn't expecting. >>>> >>>> Davide >>>> >>>> >>>> >>>> >>>> On Nov 4, 2013, at 6:42 PM, Daniel Russel wrote: >>>> >>>> It is used like any other pair score. core:: create_restraint and >>>> container::create_restraint or >>>> core::PairRrestraint/container::PairsRestraint can be used to bind it to >>>> particle pairs to make a Restraint. The container::ConsecutivePairContainer >>>> is probably useful for generating a particle pairs list. >>>> >>>> On Monday, November 4, 2013, Davide Baù wrote: >>>> >>>>> Thanks Daniel! >>>>> >>>>> The WLC class hasn't been used in forever as far as I know, but worked >>>>> fine last I looked at it. >>>>> >>>>> >>>>> Any possibility of having a example of how to use the WLC? I looked >>>>> around but did not find any. >>>>> >>>>> Thanks, >>>>> Davide >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On Wed, Oct 30, 2013 at 7:19 AM, Davide Baù davide.bau@gmail.comwrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> I would like to start using the MD and WormLikeChain functions in >>>>>> IMP, but I don't know what their current state is. >>>>>> Are they safe to use? >>>>>> >>>>>> Thanks, >>>>>> Davide >>>>>> _______________________________________________ >>>>>> IMP-dev mailing list >>>>>> IMP-dev@salilab.org >>>>>> https://salilab.org/mailman/listinfo/imp-dev >>>>>> >>>>> >>>>> _______________________________________________ >>>>> IMP-dev mailing list >>>>> IMP-dev@salilab.org >>>>> https://salilab.org/mailman/listinfo/imp-dev >>>>> >>>>> >>>>> _______________________________________________ >>>> IMP-dev mailing list >>>> IMP-dev@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-dev >>>> >>>> >>>> >>>> _______________________________________________ >>>> IMP-dev mailing list >>>> IMP-dev@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-dev >>>> >>>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >>> >>> >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >>> >>> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >> >> >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >> >> > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > >
Ah! I think I was missing the forcefield (particles were not being optimized).
On Nov 11, 2013, at 4:16 PM, Daniel Russel wrote:
> What aspect of MD would you like an example of? The MD class basically has two functions: one to set the time step and one to optimize. For the force field side there are already the charmm_forcefield examples. The bencmark_md_charmm.cpp provides a pretty simple example of using them together. > > > On Mon, Nov 11, 2013 at 3:44 AM, Davide Baù davide.bau@gmail.com wrote: > Thanks Daniel! > > Could you please provide a MD example too? > > Davide > > > On Nov 7, 2013, at 6:31 PM, Daniel Russel wrote: >> Yes, you make a pair score from WLC (using either SphereDistancePairScore or DistancePairScore) and then create a restraint. The first part you would have to do with the create_restraint function anyway. Although it might be cool to add a create_distance_restraint function. But we don't have such a thing. >> >> >> On Thu, Nov 7, 2013 at 8:51 AM, Davide Baù davide.bau@gmail.com wrote: >> Do I need to create a new PairScore class to use a WLC score with, e.g. container::PairsRestraint? >> I'm asking because the code works with existing PairScores, but they are mainly distance scores. >> >> Davide >> >> >> >> >> >> On Nov 7, 2013, at 5:21 PM, Daniel Russel wrote: >> >>> Just to add, for now just create a core::PairRestraint or containerPairsRestraint. The functionality is identical to what create_restraint would do in python (in C++ create_restraint can do cooler things with compile time binding). >>> >>> >>> On Thu, Nov 7, 2013 at 6:09 AM, Davide Baù davide.bau@gmail.com wrote: >>> That would help, thanks! >>> >>> >>> On Nov 6, 2013, at 7:08 PM, Daniel Russel wrote: >>> >>>> Sorry, the function is C++-only (as it is a template function). I could add a python version (at least should fix the docs). >>>> >>>> >>>> On Wed, Nov 6, 2013 at 9:50 AM, Davide Baù davide.bau@gmail.com wrote: >>>> There's something I don't understand: if I use IMP.container.create_restraint(), I get the attribute error "AttributeError: 'module' object has no attribute 'create_restraint'", which I wasn't expecting. >>>> >>>> Davide >>>> >>>> >>>> >>>> >>>> On Nov 4, 2013, at 6:42 PM, Daniel Russel wrote: >>>> >>>>> It is used like any other pair score. core:: create_restraint and container::create_restraint or core::PairRrestraint/container::PairsRestraint can be used to bind it to particle pairs to make a Restraint. The container::ConsecutivePairContainer is probably useful for generating a particle pairs list. >>>>> >>>>> On Monday, November 4, 2013, Davide Baù wrote: >>>>> Thanks Daniel! >>>>> >>>>>> The WLC class hasn't been used in forever as far as I know, but worked fine last I looked at it. >>>>> >>>>> Any possibility of having a example of how to use the WLC? I looked around but did not find any. >>>>> >>>>> Thanks, >>>>> Davide >>>>> >>>>> >>>>> >>>>>> >>>>>> >>>>>> On Wed, Oct 30, 2013 at 7:19 AM, Davide Baù davide.bau@gmail.com wrote: >>>>>> Hi, >>>>>> >>>>>> I would like to start using the MD and WormLikeChain functions in IMP, but I don't know what their current state is. >>>>>> Are they safe to use? >>>>>> >>>>>> Thanks, >>>>>> Davide >>>>>> _______________________________________________ >>>>>> IMP-dev mailing list >>>>>> IMP-dev@salilab.org >>>>>> https://salilab.org/mailman/listinfo/imp-dev >>>>>> >>>>>> _______________________________________________ >>>>>> IMP-dev mailing list >>>>>> IMP-dev@salilab.org >>>>>> https://salilab.org/mailman/listinfo/imp-dev >>>>> >>>>> _______________________________________________ >>>>> IMP-dev mailing list >>>>> IMP-dev@salilab.org >>>>> https://salilab.org/mailman/listinfo/imp-dev >>>> >>>> >>>> _______________________________________________ >>>> IMP-dev mailing list >>>> IMP-dev@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-dev >>>> >>>> >>>> _______________________________________________ >>>> IMP-dev mailing list >>>> IMP-dev@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-dev >>> >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >>> >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >> >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >> >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
Or just not marking the particles as optimizable? At least if you use a thermostat, things should move even with no forces. It is a bit confusing (making sure particles are optimized).... You can also pass the list of particles to be optimized explicitly to the optimizer, I kind of prefer that way.
On Mon, Nov 11, 2013 at 7:18 AM, Davide Baù davide.bau@gmail.com wrote:
> Ah! > I think I was missing the forcefield (particles were not being optimized). > > > > On Nov 11, 2013, at 4:16 PM, Daniel Russel wrote: > > What aspect of MD would you like an example of? The MD class basically has > two functions: one to set the time step and one to optimize. For the force > field side there are already the charmm_forcefield examples. The > bencmark_md_charmm.cpp provides a pretty simple example of using them > together. > > > On Mon, Nov 11, 2013 at 3:44 AM, Davide Baù davide.bau@gmail.com wrote: > >> Thanks Daniel! >> >> Could you please provide a MD example too? >> >> Davide >> >> >> On Nov 7, 2013, at 6:31 PM, Daniel Russel wrote: >> >> Yes, you make a pair score from WLC (using either SphereDistancePairScore >> or DistancePairScore) and then create a restraint. The first part you would >> have to do with the create_restraint function anyway. Although it might be >> cool to add a create_distance_restraint function. But we don't have such a >> thing. >> >> >> On Thu, Nov 7, 2013 at 8:51 AM, Davide Baù davide.bau@gmail.com wrote: >> >>> Do I need to create a new PairScore class to use a WLC score with, e.g. >>> container::PairsRestraint? >>> I'm asking because the code works with existing PairScores, but they are >>> mainly distance scores. >>> >>> Davide >>> >>> >>> >>> >>> >>> On Nov 7, 2013, at 5:21 PM, Daniel Russel wrote: >>> >>> Just to add, for now just create a core::PairRestraint or >>> containerPairsRestraint. The functionality is identical to what >>> create_restraint would do in python (in C++ create_restraint can do cooler >>> things with compile time binding). >>> >>> >>> On Thu, Nov 7, 2013 at 6:09 AM, Davide Baù davide.bau@gmail.com wrote: >>> >>>> That would help, thanks! >>>> >>>> >>>> On Nov 6, 2013, at 7:08 PM, Daniel Russel wrote: >>>> >>>> Sorry, the function is C++-only (as it is a template function). I could >>>> add a python version (at least should fix the docs). >>>> >>>> >>>> On Wed, Nov 6, 2013 at 9:50 AM, Davide Baù davide.bau@gmail.comwrote: >>>> >>>>> There's something I don't understand: if I >>>>> use IMP.container.create_restraint(), I get the attribute error >>>>> "AttributeError: 'module' object has no attribute 'create_restraint'", >>>>> which I wasn't expecting. >>>>> >>>>> Davide >>>>> >>>>> >>>>> >>>>> >>>>> On Nov 4, 2013, at 6:42 PM, Daniel Russel wrote: >>>>> >>>>> It is used like any other pair score. core:: create_restraint and >>>>> container::create_restraint or >>>>> core::PairRrestraint/container::PairsRestraint can be used to bind it to >>>>> particle pairs to make a Restraint. The container::ConsecutivePairContainer >>>>> is probably useful for generating a particle pairs list. >>>>> >>>>> On Monday, November 4, 2013, Davide Baù wrote: >>>>> >>>>>> Thanks Daniel! >>>>>> >>>>>> The WLC class hasn't been used in forever as far as I know, but >>>>>> worked fine last I looked at it. >>>>>> >>>>>> >>>>>> Any possibility of having a example of how to use the WLC? I looked >>>>>> around but did not find any. >>>>>> >>>>>> Thanks, >>>>>> Davide >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On Wed, Oct 30, 2013 at 7:19 AM, Davide Baù davide.bau@gmail.comwrote: >>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> I would like to start using the MD and WormLikeChain functions in >>>>>>> IMP, but I don't know what their current state is. >>>>>>> Are they safe to use? >>>>>>> >>>>>>> Thanks, >>>>>>> Davide >>>>>>> _______________________________________________ >>>>>>> IMP-dev mailing list >>>>>>> IMP-dev@salilab.org >>>>>>> https://salilab.org/mailman/listinfo/imp-dev >>>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> IMP-dev mailing list >>>>>> IMP-dev@salilab.org >>>>>> https://salilab.org/mailman/listinfo/imp-dev >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>> IMP-dev mailing list >>>>> IMP-dev@salilab.org >>>>> https://salilab.org/mailman/listinfo/imp-dev >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> IMP-dev mailing list >>>>> IMP-dev@salilab.org >>>>> https://salilab.org/mailman/listinfo/imp-dev >>>>> >>>>> >>>> _______________________________________________ >>>> IMP-dev mailing list >>>> IMP-dev@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-dev >>>> >>>> >>>> >>>> _______________________________________________ >>>> IMP-dev mailing list >>>> IMP-dev@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-dev >>>> >>>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >>> >>> >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >>> >>> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >> >> >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >> >> > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > >
That part should be OK (I had the same in Brownian optimizer). I noticed that in the MD the mass should be not optimizable, as I did as follow:
mk = IMP.FloatKey("mass") p.set_is_optimized(mk, True)
I will try to follow the charm examples.
Thanks! Davide
On Nov 11, 2013, at 11:07 PM, Daniel Russel wrote:
> Or just not marking the particles as optimizable? At least if you use a thermostat, things should move even with no forces. It is a bit confusing (making sure particles are optimized).... You can also pass the list of particles to be optimized explicitly to the optimizer, I kind of prefer that way. > > > On Mon, Nov 11, 2013 at 7:18 AM, Davide Baù davide.bau@gmail.com wrote: > Ah! > I think I was missing the forcefield (particles were not being optimized). > > > > On Nov 11, 2013, at 4:16 PM, Daniel Russel wrote: > >> What aspect of MD would you like an example of? The MD class basically has two functions: one to set the time step and one to optimize. For the force field side there are already the charmm_forcefield examples. The bencmark_md_charmm.cpp provides a pretty simple example of using them together. >> >> >> On Mon, Nov 11, 2013 at 3:44 AM, Davide Baù davide.bau@gmail.com wrote: >> Thanks Daniel! >> >> Could you please provide a MD example too? >> >> Davide >> >> >> On Nov 7, 2013, at 6:31 PM, Daniel Russel wrote: >>> Yes, you make a pair score from WLC (using either SphereDistancePairScore or DistancePairScore) and then create a restraint. The first part you would have to do with the create_restraint function anyway. Although it might be cool to add a create_distance_restraint function. But we don't have such a thing. >>> >>> >>> On Thu, Nov 7, 2013 at 8:51 AM, Davide Baù davide.bau@gmail.com wrote: >>> Do I need to create a new PairScore class to use a WLC score with, e.g. container::PairsRestraint? >>> I'm asking because the code works with existing PairScores, but they are mainly distance scores. >>> >>> Davide >>> >>> >>> >>> >>> >>> On Nov 7, 2013, at 5:21 PM, Daniel Russel wrote: >>> >>>> Just to add, for now just create a core::PairRestraint or containerPairsRestraint. The functionality is identical to what create_restraint would do in python (in C++ create_restraint can do cooler things with compile time binding). >>>> >>>> >>>> On Thu, Nov 7, 2013 at 6:09 AM, Davide Baù davide.bau@gmail.com wrote: >>>> That would help, thanks! >>>> >>>> >>>> On Nov 6, 2013, at 7:08 PM, Daniel Russel wrote: >>>> >>>>> Sorry, the function is C++-only (as it is a template function). I could add a python version (at least should fix the docs). >>>>> >>>>> >>>>> On Wed, Nov 6, 2013 at 9:50 AM, Davide Baù davide.bau@gmail.com wrote: >>>>> There's something I don't understand: if I use IMP.container.create_restraint(), I get the attribute error "AttributeError: 'module' object has no attribute 'create_restraint'", which I wasn't expecting. >>>>> >>>>> Davide >>>>> >>>>> >>>>> >>>>> >>>>> On Nov 4, 2013, at 6:42 PM, Daniel Russel wrote: >>>>> >>>>>> It is used like any other pair score. core:: create_restraint and container::create_restraint or core::PairRrestraint/container::PairsRestraint can be used to bind it to particle pairs to make a Restraint. The container::ConsecutivePairContainer is probably useful for generating a particle pairs list. >>>>>> >>>>>> On Monday, November 4, 2013, Davide Baù wrote: >>>>>> Thanks Daniel! >>>>>> >>>>>>> The WLC class hasn't been used in forever as far as I know, but worked fine last I looked at it. >>>>>> >>>>>> Any possibility of having a example of how to use the WLC? I looked around but did not find any. >>>>>> >>>>>> Thanks, >>>>>> Davide >>>>>> >>>>>> >>>>>> >>>>>>> >>>>>>> >>>>>>> On Wed, Oct 30, 2013 at 7:19 AM, Davide Baù davide.bau@gmail.com wrote: >>>>>>> Hi, >>>>>>> >>>>>>> I would like to start using the MD and WormLikeChain functions in IMP, but I don't know what their current state is. >>>>>>> Are they safe to use? >>>>>>> >>>>>>> Thanks, >>>>>>> Davide >>>>>>> _______________________________________________ >>>>>>> IMP-dev mailing list >>>>>>> IMP-dev@salilab.org >>>>>>> https://salilab.org/mailman/listinfo/imp-dev >>>>>>> >>>>>>> _______________________________________________ >>>>>>> IMP-dev mailing list >>>>>>> IMP-dev@salilab.org >>>>>>> https://salilab.org/mailman/listinfo/imp-dev >>>>>> >>>>>> _______________________________________________ >>>>>> IMP-dev mailing list >>>>>> IMP-dev@salilab.org >>>>>> https://salilab.org/mailman/listinfo/imp-dev >>>>> >>>>> >>>>> _______________________________________________ >>>>> IMP-dev mailing list >>>>> IMP-dev@salilab.org >>>>> https://salilab.org/mailman/listinfo/imp-dev >>>>> >>>>> >>>>> _______________________________________________ >>>>> IMP-dev mailing list >>>>> IMP-dev@salilab.org >>>>> https://salilab.org/mailman/listinfo/imp-dev >>>> >>>> >>>> _______________________________________________ >>>> IMP-dev mailing list >>>> IMP-dev@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-dev >>>> >>>> >>>> _______________________________________________ >>>> IMP-dev mailing list >>>> IMP-dev@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-dev >>> >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >>> >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >> >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >> >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
Hi,
I got both the MD and the BD to work, but there is something I don't understand about the wlc.
If I set it up and like this (with both MD and BD): > l_max = 100.0 > lp = 5.0 > wlc = IMP.misc.WormLikeChain(l_max, lp) > sd = IMP.core.SphereDistancePairScore(wlc) > crw = IMP.container.PairsRestraint(sd, cpc) > crw.set_weight(kforce) > m.add_restraint(crw)
And then check the l_max and lp values with: > sl_max = wlc.evaluate_with_derivative(l_max) > slp = wlc.evaluate_with_derivative(lp) > print "l_max %f\nlp %f" % (sl_max[0], slp[0])
I get "out of scale" values, even if wlc is the only score applied, e.g.: > l_max 590.102905 > lp 0.022517
Another thing that I noticed is that, apparently, only l_max has a influence on the final structure (it constrains the occupancy). Is that expected?
Thanks, Davide
On Nov 11, 2013, at 11:07 PM, Daniel Russel wrote:
> Or just not marking the particles as optimizable? At least if you use a thermostat, things should move even with no forces. It is a bit confusing (making sure particles are optimized).... You can also pass the list of particles to be optimized explicitly to the optimizer, I kind of prefer that way. > > > On Mon, Nov 11, 2013 at 7:18 AM, Davide Baù davide.bau@gmail.com wrote: > Ah! > I think I was missing the forcefield (particles were not being optimized). > > > > On Nov 11, 2013, at 4:16 PM, Daniel Russel wrote: > >> What aspect of MD would you like an example of? The MD class basically has two functions: one to set the time step and one to optimize. For the force field side there are already the charmm_forcefield examples. The bencmark_md_charmm.cpp provides a pretty simple example of using them together. >> >> >> On Mon, Nov 11, 2013 at 3:44 AM, Davide Baù davide.bau@gmail.com wrote: >> Thanks Daniel! >> >> Could you please provide a MD example too? >> >> Davide >> >> >> On Nov 7, 2013, at 6:31 PM, Daniel Russel wrote: >>> Yes, you make a pair score from WLC (using either SphereDistancePairScore or DistancePairScore) and then create a restraint. The first part you would have to do with the create_restraint function anyway. Although it might be cool to add a create_distance_restraint function. But we don't have such a thing. >>> >>> >>> On Thu, Nov 7, 2013 at 8:51 AM, Davide Baù davide.bau@gmail.com wrote: >>> Do I need to create a new PairScore class to use a WLC score with, e.g. container::PairsRestraint? >>> I'm asking because the code works with existing PairScores, but they are mainly distance scores. >>> >>> Davide >>> >>> >>> >>> >>> >>> On Nov 7, 2013, at 5:21 PM, Daniel Russel wrote: >>> >>>> Just to add, for now just create a core::PairRestraint or containerPairsRestraint. The functionality is identical to what create_restraint would do in python (in C++ create_restraint can do cooler things with compile time binding). >>>> >>>> >>>> On Thu, Nov 7, 2013 at 6:09 AM, Davide Baù davide.bau@gmail.com wrote: >>>> That would help, thanks! >>>> >>>> >>>> On Nov 6, 2013, at 7:08 PM, Daniel Russel wrote: >>>> >>>>> Sorry, the function is C++-only (as it is a template function). I could add a python version (at least should fix the docs). >>>>> >>>>> >>>>> On Wed, Nov 6, 2013 at 9:50 AM, Davide Baù davide.bau@gmail.com wrote: >>>>> There's something I don't understand: if I use IMP.container.create_restraint(), I get the attribute error "AttributeError: 'module' object has no attribute 'create_restraint'", which I wasn't expecting. >>>>> >>>>> Davide >>>>> >>>>> >>>>> >>>>> >>>>> On Nov 4, 2013, at 6:42 PM, Daniel Russel wrote: >>>>> >>>>>> It is used like any other pair score. core:: create_restraint and container::create_restraint or core::PairRrestraint/container::PairsRestraint can be used to bind it to particle pairs to make a Restraint. The container::ConsecutivePairContainer is probably useful for generating a particle pairs list. >>>>>> >>>>>> On Monday, November 4, 2013, Davide Baù wrote: >>>>>> Thanks Daniel! >>>>>> >>>>>>> The WLC class hasn't been used in forever as far as I know, but worked fine last I looked at it. >>>>>> >>>>>> Any possibility of having a example of how to use the WLC? I looked around but did not find any. >>>>>> >>>>>> Thanks, >>>>>> Davide >>>>>> >>>>>> >>>>>> >>>>>>> >>>>>>> >>>>>>> On Wed, Oct 30, 2013 at 7:19 AM, Davide Baù davide.bau@gmail.com wrote: >>>>>>> Hi, >>>>>>> >>>>>>> I would like to start using the MD and WormLikeChain functions in IMP, but I don't know what their current state is. >>>>>>> Are they safe to use? >>>>>>> >>>>>>> Thanks, >>>>>>> Davide >>>>>>> _______________________________________________ >>>>>>> IMP-dev mailing list >>>>>>> IMP-dev@salilab.org >>>>>>> https://salilab.org/mailman/listinfo/imp-dev >>>>>>> >>>>>>> _______________________________________________ >>>>>>> IMP-dev mailing list >>>>>>> IMP-dev@salilab.org >>>>>>> https://salilab.org/mailman/listinfo/imp-dev >>>>>> >>>>>> _______________________________________________ >>>>>> IMP-dev mailing list >>>>>> IMP-dev@salilab.org >>>>>> https://salilab.org/mailman/listinfo/imp-dev >>>>> >>>>> >>>>> _______________________________________________ >>>>> IMP-dev mailing list >>>>> IMP-dev@salilab.org >>>>> https://salilab.org/mailman/listinfo/imp-dev >>>>> >>>>> >>>>> _______________________________________________ >>>>> IMP-dev mailing list >>>>> IMP-dev@salilab.org >>>>> https://salilab.org/mailman/listinfo/imp-dev >>>> >>>> >>>> _______________________________________________ >>>> IMP-dev mailing list >>>> IMP-dev@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-dev >>>> >>>> >>>> _______________________________________________ >>>> IMP-dev mailing list >>>> IMP-dev@salilab.org >>>> https://salilab.org/mailman/listinfo/imp-dev >>> >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >>> >>> >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >> >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev >> >> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
On Thu, Nov 14, 2013 at 8:32 AM, Davide Baù davide.bau@gmail.com wrote:
> Hi, > > I got both the MD and the BD to work, but there is something I don't > understand about the wlc. > > If I set it up and like this (with both MD and BD): > > l_max = 100.0 > lp = 5.0 > wlc = IMP.misc.WormLikeChain(l_max, lp) > sd = IMP.core.SphereDistancePairScore(wlc) > crw = IMP.container.PairsRestraint(sd, cpc) > crw.set_weight(kforce) > m.add_restraint(crw) > > > And then check the l_max and lp values with: > > sl_max = wlc.evaluate_with_derivative(l_max) > slp = wlc.evaluate_with_derivative(lp) > print "l_max %f\nlp %f" % (sl_max[0], slp[0]) > > > I get "out of scale" values, even if wlc is the only score applied, e.g.: > > l_max 590.102905 > lp 0.022517 > > > Another thing that I noticed is that, apparently, only l_max has a > influence on the final structure (it constrains the occupancy). Is that > expected? > > The WLC score has a hard maximum on its max length (and goes to infinity as you approach it) and so values above that will be out of bounds. As such, you have to be pretty careful when using it so as not to have things blow up. Also, using WLC with sphere distance pair score seems a bit odd to me, but I'm not a polymer physicist :-)
In addition, it is pretty flat away from the maximum, so other than that it won't, as you are seeing, have much effect on the structure. Sorry about the slow response.
I can't find the bencmark_md_charmm.cpp file…is it under an older IMP version folder?
Davide
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Daniel Russel -
Davide Baù